The function of nucleic acids in living organisms is limited to a largely informational role. The "Central Dogma" of molecular biology, as postulated by Crick, proposes that deoxyribonucleic acid (DNA) serves as a template for the synthesis of other nucleic acids through replicative processes that "read" the information in template nucleic acids, and thus yield complementary nucleic acids, such as messenger ribonucleic acid (MRNA). mRNA then serves as a template for the translation of the information into proteins.
Most biological molecules do not specifically bind to nucleic acids. Some known exceptions are proteins (e.g., repressors, polymerases, activators, etc.) that function to transfer genetic information encoded in the nucleic acids into cellular structures and replicate genetic material. This binding depends upon the nucleotide sequence(s) that comprise the DNA or RNA involved. Short DNA sequences are known to bind to target proteins that repress or activate transcription in both prokaryotes and eukaryotes. Other short DNA sequences are known to serve as centromeres and telomeres of chromosomes, presumably by creating ligands for the binding of specific proteins that participate in chromosome mechanics.
RNA also binds some synthetic and regulatory proteins. For example, double-stranded RNA occasionally serves as a ligand for certain proteins, for example, the endonuclease RNase III from E. Coli. Proteins also bind to single-stranded RNA, although in these cases the single-stranded RNA often forms a complex three-dimensional shape that includes local regions of intramolecular double-strandedness. For example, the amino-acyl tRNA synthetases bind tightly to tRNA molecules with high specificity. As another example, a short sequence of RNA binds to the bacteriophage T4-encoded DNA polymerase. Thus, some RNA and DNA sequences are known to serve as binding partners for specific protein targets. Most known DNA binding proteins bind specifically to double-stranded DNA, while most RNA binding proteins recognize single-stranded RNA, although exceptions occur.
Nucleic acids are generally thought to have a limited range of biological activity as compared to proteins. However, some nucleic acids are known to bind target molecules other than those needed for transcription, translation and replication, and some have catalytic activity. For example, ribozymes are RNA molecules with enzymatic activity that is capable of repeatedly cleaving other RNA molecules in a nucleotide base sequence-specific manner. Such enzymatic RNA molecules can be targeted to virtually any RNA transcript, and efficient cleavage achieved in vitro (Kim et al., PNAS 84:8788 [1987]; Haseloff and Gerlach, Nature 334:585 [1988]; Cech, J. Amer. Med. Assoc., 260:3030 [1988]; and Jefferies et al., Nucl. Acids Res., 17:1371 [1989]). Ribozymes can catalyze the hydrolysis of RNA phosphodiester bonds in trans (and thus can cleave other RNA molecules) under physiological conditions. In general, enzymatic nucleic acids act by first binding to a target RNA. This binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes, and then binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA destroys its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA and is available to bind and cleave a new target. This binding and cleavage process is then multiply repeated.
Some RNA and DNA molecules have also been proven to have the ability to bind various ligands, including amino acids (Famulok et al., J. Amer. Chem. Soc., 114:3990 [1992], Connell et al., Biochem., 32:5497 [1994]), nucleotides (Connell et al., Science 264:1137 [1994], Sassanfar et al., Nature 364:550 [1993]), antibiotics (Davies et al., In Gesteland and Atkins (eds.), The RNA World, p. 185, Cold Spring Harbor Press, NY [1993]), cyanocobalamin (Lorsch et al., Biochem., 33:973 [1994]), and proteins such as the reverse transcriptase, Rev and Tat proteins of HIV (Tuerk et al., Gene 137:33 [1993]), human nerve growth factor (Binkley et al., Nucl. Acids Res., 23:3198 [1995]), and vascular endothelial growth factor (Jellinek et al., Biochem., 83:10450 [1994]).
Drugs capable of interacting with membranes have found widespread use. Perhaps the most common class of drugs that interact with membranes are ionophores. Ionophores are lipid soluble compounds capable of binding and transporting specific ions through the cell membrane. Examples of ionophores include the calcium channel ionomycin, and the antimicrobials valinomycin and gramicidin. Valinomycin forms a lipid soluble complex with K.sup.+ that readily passes through the mitochondrial membrane. Gramicidin induces the penetration of K.sup.+, Na.sup.+ and H.sup.+ through the mitochondrial membrane, causing inhibition of oxidative phosphorylation. Other ionophore antimicrobials include nonactin, nigericin, lasalocid, and monensin (See Westley, inGrayson (ed.), Antibiotics, Chemotherapeutics, and Antibacterial Agents for Disease Control, p. 301-18, John Wiley and Sons, NY [1982]). Monensin and lasalocid are commonly used as animal feed supplements to reduce the occurrence of coccidiosis and other diseases and increase feed efficiency. However, as microorganisms often rapidly become resistant to antimicrobials, new antimicrobials are constantly under development.
What is needed is the identification of nucleic acids that can be utilized to alter membrane structure and finction, as well as target effector molecules to membranes of specific cell populations.